I reciently had my lift installed, and ended up with an unfortunate outcome. The ABS and Slip indicator warning lights have now decided to stay on. Anyone have any ideas why this might be?
I had 5100s put all around, Toytec TSB AAL, and Eibach coils. (5100s@.85)
I checked the brake fluid, seems to be fine and I checked all the plugs that run into the brakes to make sure they were snug.

You have an 09 meaning you may have damaged the sensors. I found out the hard way about the vsc/abs/trac systems decided to do some odd things to me. Here is what I would suggest. Take your truck in to a dealer and ask them to do the alignment and also make sure you request to have your yaw and vsc sensors reset. This is required when toyota does alignment on the newer trucks but sometimes the mechanics forget. It does not cost anything extra. When they reset the system they basically just 0 out the values for each sensor. If a sensor was messed up it will register as error or will register as un-readable. If its error then they can just reset and your good to go. If its un-readable it means you damaged it and it will need to be replaced. The reason I suggest this is it avoids you having to go and pay them to do tons and tons of testing when this will either be a fix or tell them right away the actual problem. I faced weeks of dealership visits to fix a similar problem and that was that my computer just decided to take a vacation.

The other thing I would try is taking out your battery for a night and re-installing the next day.

R&D Custom Exhaust did the lift.
I did not unplug any of the wires from the brakes, and I do not believe they did either.
No problems when shifting to either 4H or 4L (L while in neutral anyhow)

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Try pulling the vsc/abs/trac plug from your master cyl and turn the truck on. You should have all the light turned on. Then shut your truck off and plug it back it. If nothing is wrong then your truck will have all the lights off again. If the sensor is messed up or something is wrong they will stay on. Then your going to want to have the numbers 0'd out.

As far as getting it fixed, if your abs is out just be aware that your running without abs and may be only just one tire that is the issue. This could cause somesafety problems so I would be cautious. And when you do a lift you have to do alignment anyways so get it done.

Try pulling the vsc/abs/trac plug from your master cyl and turn the truck on. You should have all the light turned on. Then shut your truck off and plug it back it. If nothing is wrong then your truck will have all the lights off again. If the sensor is messed up or something is wrong they will stay on. Then your going to want to have the numbers 0'd out.

As far as getting it fixed, if your abs is out just be aware that your running without abs and may be only just one tire that is the issue. This could cause somesafety problems so I would be cautious. And when you do a lift you have to do alignment anyways so get it done.

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The vsc/abs/trac plug I'm looking for is the plug/wires that run into each breaking system correct?

I dont quite have the same set up as you pictured, but I unplugged the wire shown and tried it. (break reservoir) No luck unfortunately
I also unplugged the Battery for about a minute, and it also didnt help. Probably need to unplug it for a bit longer if I wanted that to help though I would imagine.

^ So I would say at this point is sounds like your going to need to have them calibrate your sensors and if in the process they throw codes then you know what happened. I would prob be on the shop that did this though because they must have done some damage somehow. Make them pay for it

I got same lift setup. No warning lights. Couldn't get alignment after bc my lower control arms were seized. Got them replaced today and slip indicator came on. Could an alignment fix this or the sensor has to be reset?

You may have to do a zero point calibration after the alignment. I would also get underneath and check the abs wires. That is what ended up being my problem. The wire runs from the breaks, up into the hood where it connects to another wire. That's where mine pulled out. I just resoldered the wire and did a recalibration and it fixed the problem.